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Pathway knockout and redundancy in metabolic networks
Journal of Theoretical Biology, 2011The robustness and stability of complex cellular networks is often attributed to the redundancy of components, including genes, enzymes and pathways. Estimation of redundancy is still an open question in systems biology. Current theoretical tools to measure redundancy have various strengths and shortcomings in providing a comprehensive description of ...
Zhengzheng Pan +5 more
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Analysis of the pathway structure of metabolic networks
Journal of Biotechnology, 1999Metabolic networks comprise a multitude of enzymatic reactions carrying out various functions related to cell growth and product formation. Although such reactions are occasionally organized into biochemical pathways, a formal procedure is desired to identify the independent pathways in a bioreaction network and the degree of engagement of each ...
Brian D. Follstad +2 more
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Predicting Metabolic Pathways by Sub-network Extraction [PDF]
, 2011 Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a ...
Faust, Karoline, van Helden, Jacques
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Neural Networks for Modeling Metabolic Pathways
2021Metabolic pathways are enzyme-catalyzed reactions that can be described by the Michaelis-Menten equation. The inherent problem with Michaelis-Menten kinetics is that the model is not reversible. Reverse catalysis, which is common in metabolic pathways, can be better described by Cell Communication Protocol© which offers a Self-Organizing Map (SOM) for ...
Christoph Gille +7 more
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Inferring Meaningful Pathways in Weighted Metabolic Networks
Journal of Molecular Biology, 2006An approach is presented for computing meaningful pathways in the network of small molecule metabolism comprising the chemical reactions characterized in all organisms. The metabolic network is described as a weighted graph in which all the compounds are included, but each compound is assigned a weight equal to the number of reactions in which it ...
Jacques van Helden +4 more
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Combinatorial Complexity of Pathway Analysis in Metabolic Networks
Molecular Biology Reports, 2002Elementary flux mode analysis is a promising approach for a pathway-oriented perspective of metabolic networks. However, in larger networks it is hampered by the combinatorial explosion of possible routes. In this work we give some estimations on the combinatorial complexity including theoretical upper bounds for the number of elementary flux modes in ...
Jörg Stelling, Steffen Klamt
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Prediction of metabolic pathways from genome-scale metabolic networks
Biosystems, 2011The analysis of a variety of data sets (transcriptome arrays, phylogenetic profiles, etc.) yields groups of functionally related genes. In order to determine their biological function, associated gene groups are often projected onto known pathways or tested for enrichment of known functions.
Faust, Karoline +2 more
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From Metabolic Reactions to Networks and Pathways
2011Enzymatic reactions form a hypergraph structure and their translation into a graph structure accompanies an information loss. This chapter introduces well-known topological transformations from metabolic reactions to a graph, and discusses their advantages and disadvantages. Also discussed is the legitimacy of defining cofactors or currency metabolites,
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